Microbe-Plant interaction – Types, Examples

Microbe-Plant interaction

  • Plants are immobile, but they are continuously subjected to both biotic and abiotic stress. Constant warfare exists between harmful microorganisms and the host plant, with the outcome determining resistance or disease.
  • Plants exude a variety of organic substances, resulting in a nutrient-rich environment that is conducive to microbial growth.
  • Therefore, plants are highly colonised with a variety of microorganisms whose primary reservoir is the soil.
  • Microorganisms that colonise plants are either epiphytes (colonise plant surface) or endophytes (colonize plants interior)
  • Indirectly and directly, microbial communities affect plant growth.
  • Pathogenic, symbiotic, and associative relationships between plants and microorganisms are all possible.

Different Types of Microbe-Plant interaction

1. Pathogenic Relationship 

  • The interaction between a plant and a pathogenic microbe triggered a specific sequence of actions in the plant organism.
  • The extracellular area between the cell wall and plasma membrane serves as the initial battleground for plants and pathogens. In the first phase of an infection, the bacteria, fungi, viruses, and oomycetes that colonise the living plant tissues are enclosed in this tight area.
  • Therefore, it is thought that the apoplastic area mediates the initial cross-talk between host and pathogen.
  • In this apoplastic zone, the final relationship between the host and pathogen is determined by interactions between the proteins and other metabolites released by both the host and the pathogen.
  • Pathogen types depending on their effects:
    1. Necrotrophy : plant cells are killed 
    2. Biotrophy: plant cells remain alive 
    3. Hemibiotrophy: plant cells initially alive later killed. 

2. Symbiotic relationships 

  • Symbiosis refers to partnerships between creatures of various species that exhibit a close association.
  • At least one of the collaborating species in symbiotic interactions enjoys a nutritional advantage.
  • According to the nature of the relationship, three types of symbiosis have been recognised.
    1. Mutualism 
    2. Commensalism 
    3. Parasitism 

a. Mutualism 

  • Mutualism is a biological connection between two organisms in which they mutually benefit.
  • The discovery of this phrase was made by Pierre van Benden.
  • They may be able to live independently, despite exchanging food or providing shelter or safety.

Mutualism examples 

There are numerous instances of mutualistic relationships:

  • Microorganisms and Plants: Rhizobium in root nodules.
  • Protists and Fungi: for instance, Lichen Terrestrial plants and insects: for instance, Pollination

b. Commensalism 

  • Commensalism is the interaction between two different species in which one species benefits and the other is neither damaged nor benefited by the relationship.
  • It is extremely improbable that two species may coexist without affecting one another, hence such partnerships are extremely uncommon.
  • The majority of examples of commensalism include feeding or protection.

Commensalism Example

  • Barnacles cling to the whale or shark’s skin. The association helps the barnacle, which neither harms nor aids its host.

c. Ammensalism 

  • Ammensalism is the ecological interaction in which one species does harm to another without receiving any benefit in return.
  • This form of symbiotic interaction is prevalent, but it is not considered a significant process in community structure because it is unintentional and provides no advantage to the species causing the injury.

Ammensalism examples 

  • Many species of fish and other animals can perish as a result of algal blooms, although the algae do not gain from their deaths.
  • The roots of black walnut trees release a substance that inhibits the growth of nearby trees.
  • Elephants trampling on ants or levelling brush are detrimental to the elephant, but beneficial to the ants and brush. 

3. Parasitism

  • Parasitism is an interaction in which one creature, the parasite, obtains nutrition from another organism, the host.
  • Therefore, parasites are chemoautotrophs.
  • This relationship is detrimental to the host, however a true parasite does normally not kill its host.

4. Synergism 

  • Interaction or collaboration between two or more organisations, substances, or other agents to produce an effect greater than the sum of their individual effects.
  • For instance, E.coli, which receives nutrients from dietary materials consumed by the host, creates vitamins that are utilised by the host.
  • In the manufacturing of yoghurt, the synergistic effect of Lactobacillus bulgaricus and Streptococcus thermophillus.


  • The rhizosphere is the small soil zone directly impacted by root exudates and connected with soil microorganisms.
  • Numerous bacteria and other microbes in the rhizosphere feed on rhizodeposition, often known as shed plant cells, and the proteins and sugars generated by roots.
  • As a result of root exudates and microbial communities, the majority of nutrient cycling and disease control required by plants happens in close proximity to roots.
  • Additionally, the rhizosphere provides area for the production of allelochemicals to govern neighbouring and related plants.
    • Rhizoplane: Area on the surface of root.
    • Outer rhizoplane: Outer area on the surface of root 
    • Inner rhizoplane: Inner area of the surface of root 

Non – Rhizosphere 

  • The zone distant from a plant’s roots.
  • It is an area distant from the root systems of living plants.
  • The area of soil that is not affected by plant roots.
  • In the proximity of plant roots, a lower level of microbial activity prevails than in the surrounding soil.

R:S Ratio 

  • R refers to the rhizosphere’s soil.
  • S refers to the non-rhizosphere soil.
  • The R:S ratio is the ratio of the microbial population per unit weight of rhizosphere soil (R) to the microbial population per unit weight of adjacent non-rhizosphere soil (S) (S).
  • Rhizosphere microbiological activity is far more intense than non-rhizosphere microbiological activity.
  • It is possible to determine the qualitative and quantitative characteristics of rhizosphere and non-rhizosphere microorganisms.
  • The R:S ratio can be computed and stated in terms of the number of microorganisms per gramme of rhizosphere and non-rhizosphere soil.

Rhizosphere Effect

  • The stimulation of the growth of a soil microorganism as a result of physical and chemical change of the soil and the contribution of root excrement and organic waste inside a rhizosphere.
  • Bacteria have a greater rhizosphere influence than actinomycetes and fungi. Protozoa and algae exhibit just a minor effect.
  • In general, gram-negative, non-sporulating, rod-shaped bacteria predominate in the root zone.
  • Agronomically speaking, the rhizosphere has an abundance of nitrogen-fixing and phosphate-solubilizing microorganisms.
  • The microbial biomass within the rhizosphere functions as both a source and a sink for plant nutrients.
  • Rhizosphere microorganisms are influenced by plant type, the nature of root exudates, and soil conditions. 


  • In microbiology, the term phyllosphere refers to the whole above-ground sections of plants that serve as a habitat for microorganisms.
  • Phyllosphere may provide a niche for nitrogen fixation and the release of chemicals that promote plant growth.
  • Phyllosphere is typically referred to as the young field that covers the surface of fragile leaves.
  • Young leaf surface is responsible for the majority of leaf exudates and leaf diffusates.
  • Typically, leaf exudates contain sugars (glucose, fructose, and sucrose) and indole acetic acid.


  • In the spermosphere, interactions between the soil, microbial populations, and germinating seeds occur.
  • During the germination process, a variety of bacteria wrap the surface of the seeds.
  • The microbial communities present in the spermosphere may directly reflect those of the germination media or are host-dependent and quantitatively and qualitatively affected by exudates from the host.
  • Important spermosphere microorganisms include several nitrogen-fixing microorganisms, organic acid-producing microorganisms, growth substance-producing microorganisms, and similar microorganisms.

Factors influencing Rhizospheric microorganisms

  1. Soil type and moisture: In general, microbial activity and population are highest in the rhizosphere region of plants grown in sandy soil and lowest in high humus soil, and there are more rhizosphere microorganisms when soil moisture is low.
  2. Soil amendment and fertiliser: Crop leftovers, animal manure, and chemical fertilisers added to the soil had no discernible impact on the quantitative or qualitative changes in the rhizosphere microbiota. In general, the nature of plants is more essential than soil fertility.
  3. Soil pH: The respiration of rhizosphere microorganisms may influence the pH of the rhizosphere soil. If the activity and population of rhizosphere microorganisms are greater, then the rhizospheric pH is lower than that of the surrounding soil. Rhizosphere impact for bacteria and protozoa is soil that is slightly more alkaline, whereas that for fungi is soil that is more acidic.
  4. Proximity of root with soil: The Rhizosphere impact diminishes dramatically as the distance between plant roots and soil increases.
  5. Plant species: Variations in rooting habitat, tissue composition, and excretory products account for the qualitative and quantitative variances among plant species. In general, legumes exhibit or generate a more prominent rhizosphere influence than grasses or cereals.
  6. Age of plant: The quantity of rhizosphere microflora grows with the plant’s age, peaking during blooming, the most active stage of plant development and metabolism.
  7. Root exudates or excretion: It is one of the most essential factors responsible for the availability of a wide range of organic compounds at the root region, via root exudates or excretion.

Plant Growth Promoting Rhizobacteria (Pgpr) 

  • Typically, rhizobacteria are known as Plant Growth Promoting Rhizobacteria.
  • Rhizobacteria are symbiotic bacteria that colonise the roots of several plants.
  • PGPRS have diverse interactions with various host plant species.
  • PGPRS enhance plant growth by direct and indirect means, but specific mechanisms involved have not all been well characterized.
  • The PGPRS improve plant growth by fixing nitrogen through nitrogen fixation.
  • As biofertilizers, they are an important group of microorganisms.
  • Some of the PGPRS are Rhizobacteria, Pseudomonas, Azotobacter, Azospirillum etc.


  • A mycorrhiza is a symbiotic relationship between the roots of a vascular host plant and a fungus.
  • The plant absorbs solar energy through chlorophyll and transfers it to the fungus, which in turn provides the plant with water and mineral nutrients from the soil.
  • This marriage takes occur in the plant’s roots.
  • Some plant families, such as Brassicaceae and Chenopodiaceae, are ineligible for membership in this club.
  • Mycorrhiza are typically classified as > Ectomycorrhizas > Endomycorrhizas.
  • On the basis of hyphae’s penetration into root cells, the two types are distinguished.


  • In ectomycorrhizal association, the fungus produces a mantle or sheath over the fine lateral roots of the host tree and shoots some hyphae into the intercellular spaces of the outer cortex to form a so-called Hartignet.
  • Arbuscules and vesicles, which are characteristic of endomycorrhizae, are not found. The fungi-covered lateral roots frequently adopt a bloated or coral-like appearance.
  • In reforestation, ectomycorrhizal fungi are of enormous importance. In developing pine forests, the seedlings are always inoculated with soil containing the right ectomyct rhizal fungal strains.
  • Compared to non-mycorrhizal plants, trees with ectomycorrhizal association can grow better under nutrient-deficient situations due to their enhanced ability to absorb nutrients from the soil.
  • Numerous forest trees, including conifers such as Pinus, Cedrus, and Abies and deciduous non-conifers such as oak, beech, birch, etc., develop ecto-mycorrhizal partnerships. Additionally, the fungal components belong to several groupings of primarily higher fungus.
  • Common basidiomycetes include agarics and gasteromycetes. Ascomycetes-related truffles are able to connect with pines.
  • Common genera of ecto-mycorrhizal fungi include Russula, Clitocybe, Boletus, Lactarius, and Tuber, among others.

Endomycorrhizal Fungi

  • Endomycorrhizal associations are more prevalent than ecto-mycorrhizal associations and are found in nearly all plant families.
  • Orchid endo-mycorrhizae are the most well-known endo-mycorrhizae. It is common knowledge that under natural conditions, orchids cannot thrive without the presence of fungi.
  • Endomycorrhizal fungi invade root cells and are often confined to the cortical region, crossing the endodermis only infrequently.
  • Within the cells, the vesicular-arbuscular types form distinctive structures. After growing in the cells for a period of time, these structures degenerate and finally breakdown, thereby nourishing the host. Thus, the plant host immediately benefits from VAM.
  • Endomycorrhizal fungi are completely limited to plant roots and never infect the plant’s leaves.
  • Possibly, an inhibitory substance produced by the green sections stops fungi from invading the aerial parts. This is indicated by the absence of fungal development directly beneath the plant’s aerial portions.
  • Frequently, the identity of the endo-mycorrhizal fungi is unknown. Components include phycomycetes, as demonstrated by the aseptate structure of the hyphae, and higher fungi, including basidiomycetes and fungi imperfecti.
  • Numerous species of orchids and Ericaceae have phycomycetous fungi, however Gastrodiaelata is known to be associated with the basidiomycetes Armillaria mellea.
  • This orchid will not bloom until it forms a relationship with the fungus. Other orchids are known to produce endomycorrhiza with Rhizoctonia species, including R. repens.
  • Among VAM fungi, species of Pythium have been discovered in numerous Liliaceae species. Endogone has been identified as a fungal component of VAM in apple, strawberry, and other plant species.
  • VAM has been discovered in numerous monocot and dicot Gramineae, Leguminosae, Compositae, Palmae, etc. species.


  • Dolatabadian A. Plant-Microbe Interaction. Biology (Basel). 2020 Dec 30;10(1):15. doi: 10.3390/biology10010015. PMID: 33396600; PMCID: PMC7823258.
  • Wu CH, Bernard SM, Andersen GL, Chen W. Developing microbe-plant interactions for applications in plant-growth promotion and disease control, production of useful compounds, remediation and carbon sequestration. Microb Biotechnol. 2009 Jul;2(4):428-40. doi: 10.1111/j.1751-7915.2009.00109.x. Epub 2009 Apr 23. PMID: 21255275; PMCID: PMC3815904.
  • Vishwakarma, K., Kumar, N., Shandilya, C., Mohapatra, S., Bhayana, S., & Varma, A. (2020). Revisiting Plant–Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review. Frontiers in Microbiology, 11. doi:10.3389/fmicb.2020.560406 
  • Augusta, A. C. , Bertha, E. C. , & Eromosele, A. S.  (2022). Plant-Microbe Interaction: Prospects and Applications in Sustainable Environmental Management. In  (Ed.), Plant Hormones – Recent Advances, New Perspectives and Applications. IntechOpen.
  • Singh, P. P., Kujur, A., Yadav, A., Kumar, A., Singh, S. K., & Prakash, B. (2019). Mechanisms of Plant-Microbe Interactions and its Significance for Sustainable Agriculture. PGPR Amelioration in Sustainable Agriculture, 17–39. doi:10.1016/b978-0-12-815879-1.00002-1 
  • Noman, A., Aqeel, M., Qasim, M., Haider, I., & Lou, Y. (2019). Plant-insect-microbe interaction: A love triangle between enemies in ecosystem. Science of The Total Environment, 134181. doi:10.1016/j.scitotenv.2019.134181 
  • Perreault, R., Laforest-Lapointe, I. Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene. ISME J 16, 339–345 (2022).
  • Imam, J., Singh, P. K., & Shukla, P. (2016). Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications. Frontiers in Microbiology, 7. doi:10.3389/fmicb.2016.01488 

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